Flanagan, who was a decorated serviceman in the Second World War before making his name as a footballer, played 163 games for the Cats over nine seasons.
"Fred was a great man and a great Geelong man," Geelong chief executive Brian Cook said on Monday.
"He loved the club and the people that made up the club. I never heard anyone say a bad word about Fred and he loved footy as much at the end as he did throughout his life.
"Fred's record as a player speaks for itself, but it is the man himself that was special.
"We will all miss Fred’s friendship and we offer our deepest condolences to Pauline and to their family."
Recruited from the northern Victorian town of Swan Hill, Flanagan played his first VFL game against Melbourne at the Punt Road Oval (the MCG was still being converted from an army base back to a sporting arena) in round one, 1946.
Then aged 22, he quickly developed a reputation as a high-flying key forward whose marking and kicking were the highlights of his game.
Nicknamed "Troubles" because he was always worrying, Flanagan enjoyed a brilliant playing career.
He won Geelong's best and fairest in 1949, finished second in the Brownlow Medal in 1950 (he polled 88 Brownlow votes in all) and topped the Cats' goalkicking in 1954.
Geelong's captain in 1949 and between 1951 and '53, he led the Cats in three Grand Finals, winning the first two and losing the last one to a Lou Richards-led Collingwood side.
Flanagan also played for Victoria in each of his first eight seasons.
In all, he played 22 representative games for Victoria, including a year as captain-coach in 1952.
Business commitments forced Flanagan to retire while still in top form. His last game was against Fitzroy at the Brunswick Street Oval in round four, 1955.
One of the Cats' most revered former stars, he received a host of honours in the past two decades.
He was inducted into the Australian Football Hall of Fame in 1998 and was later named in Geelong's team of the century.
Flanagan was heavily involved in the club's past players' group. He also served the club as patron of the Geelong Cats Forever bequest program and was a trustee of the Geelong Cats Sports Foundation from its inception until 2008.
A long-standing member of Pivots coterie group, Flanagan regularly attended training sessions and took an active interest in current players, especially those wearing his former No. 10 jumper.
He sent a letter of encouragement to Geelong's current No. 10, Daniel Menzel, when the youngster was injured last year.
Adam McNicol covers Geelong news for AFL.com.au. Follow him on Twitter at @AFL_AdamMcNicol
